Ok so I sorted mine out couple of moments ago.
The problem with the missaligned motor shaft still persisted no matter how much I played with the climate panel temp buttons, it was basically 180 degrees out of sync.
So, according to what someone said here about the gears in the motor assembly, I did it like this:
Started the car, climate on full cold and on Auto setting.
*note: the cog is rotated towards of the car when on full cold so I spun it in that direction by hand.
This was with both motors wired, to set their shafts in that particular setting.
Stopped the car and the climate also. Now I disconnected the missaligned motor - it's held onto that plate by two 6mm screws, identical to the other 3 that keep the entire plate in place.
After moving a little bit by hand the white gears controlling the vents I quickly managed to align the remaining motor (the one without the problem) to it's white cog and install the plate in place. I only used 2 screws to keep the plate in place.
I made sure once again that the damaged (and cable tie repaided cog) is rotated to the front all the way (cold air setting).
Now, when you hold the motor in your hand you'll see that it has 3 pins holding it to it's gear mechanism and shaft, you can easily take it apart carefully with 2 thin flathead screwdrivers.
After you do this, you will be able to rotate the shaft in the gearhousing accordingly and install the gear mechanism ONLY to the main plate, carefully aligning it to the cog. Having the motor detached this will be very easy to do. Then, just bolt down the gear housing with the 2 screws and then clip the motor onto it carefully, don't rush this in order to prevent damage to the inner plastic gears.
Plug the power supply back to the motor and bingo!
Now startd the car and test the climate control buttons to make sure it all works.
Mine did
Ok so now the question is:
Why is this happening? asw far as I can judge there can be 2 scenarios:
1. the ceiling temp sensor reads badly, tricking the motor to try and rotate the cog to the cold air setting more and more untill it snaps
2. Maybe the motor itself goes bananas little by little and puts pressure on the cog that eventually causes the same issue - SNAP!
Given this, can we prevent this from happening again somehow?
Cheers!